Modify Scaffold class skeleton

.gitignore

@@ -0,0 +1,162 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
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+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
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+.spyderproject
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+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

.pre-commit-config.yaml

@@ -13,6 +13,7 @@ repos:
             "--line-length=120",
             "--fix"
           ]
+        exclude: "__init__.py"
       - id: ruff
         name: Ruff lint - complexity analysis
         description: "Run ruff for code complexity analysis"

src/sparc_imp/__init__.py

@@ -1 +1,2 @@
-from scaffold import Scaffold
+from sparc_imp.mesh import Mesh
+from sparc_imp.scaffold import Scaffold

src/sparc_imp/mesh.py

@@ -0,0 +1,3 @@
+class Mesh(object):
+    def __init__(self) -> None:
+        pass

src/sparc_imp/scaffold.py

@@ -1,67 +1,54 @@
-class Scaffold:
-    """
-    Scaffold  
-    """
-    def __init__(self,):
-        """
-        this is my constructor
-        """
-        pass
+from typing import List
 
-    def read_ds(self, derivative_dir):
-        """ 
-        Load the scaffold from the .json files in the derivative directory.
-        :param derivative_dir: The directory containing the .json files
-        :type derivative_dir: str
-        :return:
-        :rtype:
-        """
-        pass 
+import pyvista as pv
 
-    def plot(self, scaffold_tag=None): 
+from sparc_imp import Mesh
 
-        """   
-        Displays the meshes in the scaffold belonging to the scaffold_tag.
-        :param scaffold_tag: The tag of the meshes in the scaffold to be plotted
-        :type scaffold_tag: list of str
-        :return: 
-        :rtype: 
-        """ 
-        if scaffold_tag is None:  
-            assert self.scaffold_tag is not None, "scaffold_tag is not defined" # To-Do: The scaffold tags should be added during loading
-            scaffold_tag = self.scaffold_tag
-        pass 
 
-    def metadata(self, ): 
-        """ 
-        Displays the metadata of the scaffold. 
-        :return: 
-        :rtype: 
-        """
-        pass 
+class Scaffold(object):
+    meshes: List[Mesh]
 
-    def export(self, results_dir): 
-        """
-        Exports the scaffold to the results directory as VTK files.
-        """ 
-        pass 
+    def __init__(self, name):
+        self._name = name
 
-    def add_mesh(self, mesh, label): 
-        """
-        Adds a mesh to the scaffold.
-        :param mesh: The mesh to be added
-        :type mesh: Mesh
+    def build_scaffold(self, dir: str) -> pv.PolyData:
+        """Create Scaffold from existing meshes and geometry.
+
+        Args:
+            dir (str): Root directory for derivative files where JSONs are.
+
+        Returns:
+            pv.PolyData: Scaffold containing Geometry and meshes
         """
-        pass 
+        return
+
+    def plot(self):
+        """Plot the scaffold with all meshes along with checkboxes to activate
+        or deactivate meshes."""
+        return
+
+    def export(self, output_filepath: str = "output.vtk"):
+        """Export the scaffold to a .vtk file
 
-    def get_mesh_ids(self, scaffold_tag): 
+        Args:
+            output_filepath (str, optional): output_filepath (str): Output file
+            path to save .vtk file. Defaults to "output.vtk".
         """
-        Returns the mesh ids of the scaffold belonging to the scaffold_tag.
-        :param scaffold_tag: The tag of the meshes in the scaffold
-        :type scaffold_tag: list of str
-        :return: 
-        :rtype: 
+
+    def get_metadata(self):
+        """Show a tabular view of metadata that is important to the user"""
+        return
+
+    def add_mesh(self, mesh_name: str, mesh: Mesh):
+        """Modify self.meshes and add a new mesh to the list.
+
+        Args:
+            mesh_name (str): User defined name for the mesh
+            mesh (Mesh): Mesh containing new experimental data
         """
-        pass  
+        return
 
-
+    def get_mesh_ids(self):
+        """List all meshes with their corresponding user defined names. These IDs
+        could be used later on for different mesh specific tasks."""
+        return